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I got the following error during scaffold step.
---
************************_ERROR**_********************************
During scaffold, the following command failed with return code -6:
> > /tmp/_ME…
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The command used was
/data/home/nsarode3/MetAmos/metAMOS_binary/runPipeline -m bowtie2 -g MetaGeneMark -c phymmbl -p 10 -d /data/home/nsarode3/metamos_trial/stn1_11mts_metamos_trial_PhymmBL/
Select…
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Hello,
I attempted running the pipeline and got "MissingInputFileError:". It looks as if after assembly, the necessary files are not generated. But am not sure if this is any problem with MetaGeneMark…
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Hi folks,
I'm having an issue running metamos on our linux 64bit machine. Running the following command, my run died after chugging away at FragGeneScan for several days.
The command I ran was:
~/sof…
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Apparently, pybedtools needs cython to continue, but pybedtools is installed BEFORE cython.
moving the cython requirement in config/python-libs.yaml to be before pybedtools appears to resolve the i…
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When we use your http://data.okfn.org/ Here http://senegalouvert.org/ , I have problem to active The ---embed for graph --- for selected data http://senegalouvert.org/data ,
http://senegalouver…
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I need to use a python version that is not /usr/bin/python to get ruffus to work.
You could change the shebang at the top of the sga-pipeline python script from:
# !/usr/bin/python
to:
# !/usr/bin/e…
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Dear all,
When I try to run metAMOS on test data like this:
[jjin01@tll-rv2 MetaAMOS]$ /data/apps/metAMOS/./runPipeline -a soap -c fcp -g fraggenescan -p 15 -d test1 -k 55 -t -f Assemble,MapReads,Fi…
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Hi,
I getting the following error probably in the classify step:
Starting Task = classify.CLASSIFY
**\* metAMOS running command: perl -I /home/bioinfo/programas/metAMOS-1.5rc1/AMOS/Linux-x86_64/lib …
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Occasionally I have samples where some of the contigs in my reference assembly have zero coverage. When this happens I observe the following error at the FindORFS stage:
```
Traceback (most recent ca…